library(dplyr)
library(tidyr)
library(ggplot2)
library(ggtext)
theme_set(theme_minimal())
Contemplating about the weather, I wondered if I could find out the “most unusual” and “most ideal” years regarding air temperature in Germany, i.e. if I could identify the years in which the daily temperature deviated the most and the least from the expected seasonal temperature. So I decided to look into historical climate data, created an extremely simplified seasonal temperature model and then investigated the deviations from that model. Although it’s all quite simple, this little exploration gives some insights into how and why we can use a linear model for such data.
I retrieved the historical climate data for a weather station in Berlin-Dahlem (a bit outside the city) from 1950 to now from the German Meteorological Service (Deutscher Wetterdienst – DWD). The data come as delimited files with semicolon as column separator. Historical data until 2022 and present data from 2022 to now come as separate files.
raw_hist <- read.delim('data/produkt_klima_tag_19500101_20221231_00403.txt', sep = ';')
head(raw_hist)
## STATIONS_ID MESS_DATUM QN_3 FX FM QN_4 RSK RSKF SDK SHK_TAG NM VPM
## 1 403 19500101 -999 -999 -999 5 2.2 7 -999 0 5.0 4.0
## 2 403 19500102 -999 -999 -999 5 12.6 8 -999 0 8.0 6.1
## 3 403 19500103 -999 -999 -999 5 0.5 1 -999 0 5.0 6.5
## 4 403 19500104 -999 -999 -999 5 0.5 7 -999 0 7.7 5.2
## 5 403 19500105 -999 -999 -999 5 10.3 7 -999 0 8.0 4.0
## 6 403 19500106 -999 -999 -999 5 7.2 8 -999 12 7.3 5.6
## PM TMK UPM TXK TNK TGK eor
## 1 1025.6 -3.2 83 -1.1 -4.9 -6.3 eor
## 2 1005.6 1.0 95 2.2 -3.7 -5.3 eor
## 3 996.6 2.8 86 3.9 1.7 -1.4 eor
## 4 999.5 -0.1 85 2.1 -0.9 -2.3 eor
## 5 1001.1 -2.8 79 -0.9 -3.3 -5.2 eor
## 6 997.5 2.6 79 5.0 -4.0 -4.0 eor
raw_pres <- read.delim('data/produkt_klima_tag_20221107_20240509_00403.txt', sep = ';')
head(raw_pres)
## STATIONS_ID MESS_DATUM QN_3 FX FM QN_4 RSK RSKF SDK SHK_TAG NM VPM
## 1 403 20221107 -999 -999 -999 10 0.0 6 4.5 0 6.2 9.6
## 2 403 20221108 -999 -999 -999 10 0.2 6 7.5 0 6.0 10.4
## 3 403 20221109 -999 -999 -999 10 1.0 6 3.7 0 6.6 11.4
## 4 403 20221110 -999 -999 -999 10 0.0 0 6.1 0 5.1 10.2
## 5 403 20221111 -999 -999 -999 10 0.0 0 1.9 0 6.3 9.6
## 6 403 20221112 -999 -999 -999 10 0.0 0 7.3 0 4.0 8.8
## PM TMK UPM TXK TNK TGK eor
## 1 1002.9 10.7 75 15.0 6.4 5.1 eor
## 2 1002.7 12.1 75 16.9 7.9 4.2 eor
## 3 1001.5 11.8 83 15.0 9.0 5.1 eor
## 4 1012.6 11.7 74 14.3 8.6 5.8 eor
## 5 1020.1 8.6 87 12.8 4.0 0.6 eor
## 6 1022.8 6.4 92 13.8 1.8 -0.9 eor
After reading in the files, we merge them, select only the necessary variables, transform the dates and remove duplicates (since the historical and the present data both contain observations from 2022) to generate our final measurements dataset meas:
meas <- bind_rows(raw_hist, raw_pres) |>
select(date = MESS_DATUM, temp = TMK) |> # TMK is day-time average temperature in °C
mutate(date = as.POSIXct(strptime(date, "%Y%m%d")),
year = as.integer(as.numeric(format(date, "%Y"))),
day = as.integer(as.numeric(format(date, "%j")))) |> # day of the year as decimal number from 1 to 366
distinct(date, .keep_all = TRUE) # remove duplicates
rm(raw_hist, raw_pres) # don't need the raw data any more
stopifnot(all(count(meas, date)$n == 1)) # make sure there are no duplicates
head(meas)
## date temp year day
## 1 1950-01-01 -3.2 1950 1
## 2 1950-01-02 1.0 1950 2
## 3 1950-01-03 2.8 1950 3
## 4 1950-01-04 -0.1 1950 4
## 5 1950-01-05 -2.8 1950 5
## 6 1950-01-06 2.6 1950 6
Let’s visualize the time series with a simple plot. I will also add a smoothed curve showing an overall trend, which indicates a nearly linear increase in average yearly temperature by about 2°C since the 1950’s. I’ll later come back to that. We can also see the typical seasonal changes.
ggplot(meas, aes(date, temp)) +
geom_line() +
geom_smooth(method = "gam") +
labs(title = "Daily day-time average temperature in Berlin-Dahlem over time",
x = "",
y = "Temperature in °C")
Figure 1: Daily day-time average temperature in Berlin-Dahlem over time
The periodical temperature changes can be visualized by by looking at a smaller time frame:
filter(meas, year >= 2018) |>
ggplot(aes(date, temp)) +
geom_line() +
geom_smooth(span = 0.2, method = "loess") +
labs(title = "Daily day-time average temperature in Berlin-Dahlem since 2018",
x = "",
y = "Temperature in °C")
We can also plot the yearly trend by plotting the temperature against the day of the year. We can see the typical seasonal pattern but also the slight overall increase in temperature over the years, since more recent years (yellow color) tend to have higher temperatures, especially in the winter.
ggplot(meas, aes(day, temp, color = year)) +
geom_line(alpha = 0.25) +
scale_color_binned(name = "Year", type = 'viridis') +
labs(title = "Daily day-time average temperature in Berlin-Dahlem over time",
x = "Day of the year",
y = "Temperature in °C")
Figure 2: Daily day-time average temperature in Berlin-Dahlem over time
Naturally, and confirmed with the above plots, we can use a periodic function like the cosine function to model these temperatures. In general this periodic function can be written as
\[\begin{equation} y = c \cos (x + \varphi), \tag{1} \end{equation}\]
where \(c\) controls the amplitude (maximum spikes), \(\varphi\) the phase (shift on the x-axis) and \(x\) the frequency. With a linear model, we can only fit linear terms like \(y = ax + b\), so we have the problem that we can’t estimate the frequency and the phase. Luckily – in our very simple case – the frequency is already known: the seasonal pattern repeats yearly, so we can calculate \(x = 2 \pi D / 366\), where \(D\) is the day of the year. Because of leap years, \(D\) can range from 1 to 366 and so we divide it by 366. This means that over the course of a year, \(x\) makes “a full circle” from above 0 to \(2 \pi\).
The second problem – that we can’t estimate the phase with a linear model directly – can be solved by applying a neat trick that transforms the cosine wave with an amplitude and a phase shift to a linear combination of a cosine and a sine wave:
\[\begin{equation} c \cos (x + \varphi) = a \cos x + b \sin x, \tag{2} \end{equation}\]
where
\[ c = \text{sgn}(a) \sqrt{a^2 + b^2}, \\ \varphi = \arctan \frac{-b} a. \]
This means we can estimate \(a\) and \(b\) as coefficients for the above linear combination that is equivalent to the initially defined cosine wave. Hence we can finally specify our linear model m1 for the temperatures \(Y_t\) as
\[\begin{equation} Y_t = \beta_0 + \beta_1 \cos(x_t) + \beta_2 \sin(x_t) + \epsilon_t, \tag{3} \end{equation}\]
where \(x_t\) is the only regressor – the day of the year transformed to range \((0, 2 \pi]\) as described above –, \(\beta_0\) to \(\beta_2\) are the coefficients we seek to estimate and \(\epsilon_t\) is the error term.
We can now estimate the model m1 in R by first computing \(x_t\) and then using lm to fit the model using our measurements meas:
# compute frequency x
meas <- mutate(meas, x = 2 * pi * day/366)
# fit the model
m1 <- lm(temp ~ cos(x) + sin(x), meas)
summary(m1)
##
## Call:
## lm(formula = temp ~ cos(x) + sin(x), data = meas)
##
## Residuals:
## Min 1Q Median 3Q Max
## -18.3493 -2.5635 -0.0229 2.5823 14.0507
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 9.41121 0.02290 410.93 <2e-16 ***
## cos(x) -9.00711 0.03244 -277.66 <2e-16 ***
## sin(x) -2.55724 0.03234 -79.08 <2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 3.774 on 27155 degrees of freedom
## Multiple R-squared: 0.7544, Adjusted R-squared: 0.7544
## F-statistic: 4.17e+04 on 2 and 27155 DF, p-value: < 2.2e-16
The model has a decent fit given its simplicity: About 75% of the variation of the temperature can be explained by the seasonal pattern we modeled with the periodic functions. The estimated intercept reflects the mean of the temperature and the coefficients for the periodic functions result in the oscillation around the mean.
We can see that for predicted values near 0°C the errors are a bit larger and also the distribution of the errors is slightly left skewed.
plot(m1, which = 1:2, ask = FALSE)
Let’s plot the model predictions of the temperatures on top of the measured values. For a better overview, we only consider data from 2018 or newer:
meas_fit <- cbind(meas, pred = fitted(m1))
filter(meas_fit, year >= 2018) |>
ggplot() +
geom_line(aes(date, temp), alpha = 0.25) +
geom_line(aes(date, pred), color = 'red') +
labs(title = "Daily day-time average temperature in Berlin-Dahlem since 2018",
subtitle = "Model predictions in <span style='color:red'>red</span>.",
x = "",
y = "Temperature in °C") +
theme(plot.subtitle = element_markdown())
Let’s show that we can again apply the transformation in equation (2) so that we can recover the cosine wave form in equation (1) from the linear combination form of the model equation (3). As expected, we get same predictions from both model representations:
a <- m1$coefficients[2]
b <- m1$coefficients[3]
# calculate c and phi from the coefficients a and b
c <- sign(a) * sqrt(a^2 + b^2)
phi <- atan(-b/a)
# predictions from the cosine wave form of the model equation for model m1
meas_fit$pred2 <- m1$coefficients[1] + c * cos(meas$x + phi)
filter(meas_fit, year >= 2018) |>
ggplot() +
geom_line(aes(date, temp), alpha = 0.25) +
geom_line(aes(date, pred), color = 'red') +
geom_line(aes(date, pred2), color = 'blue', linetype = "dashed") +
labs(title = "Daily day-time average temperature in Berlin-Dahlem since 2018",
subtitle = "Model predictions in <span style='color:red'>red (linear combination form)</span>
and <span style='color:blue'>blue (cosine wave form)</span>.",
x = "",
y = "Temperature in °C") +
theme(plot.subtitle = element_markdown())
Let’s plot the model predictions for the whole time range.
ggplot(meas_fit) +
geom_line(aes(date, temp), alpha = 0.25) +
geom_line(aes(date, pred), color = 'red') +
labs(title = "Daily day-time average temperature in Berlin-Dahlem over time",
subtitle = "Model predictions in <span style='color:red'>red</span>.",
x = "",
y = "Temperature in °C") +
theme(plot.subtitle = element_markdown())
It’s barely visible at this scale, but the model systematically overestimates temperatures around the beginning of the time range and underestimates temperatures towards the end of the time range. We can see this more clearly with a plot similar to figure 2. Temperatures before 1970 (dark purple) tend to be overestimated while temperatures from 2000 and later tend to be underestimated:
ggplot(meas_fit, aes(day, temp, color = year)) +
geom_line(alpha = 0.25) +
geom_line(aes(day, pred), color = 'red') +
scale_color_binned(name = "Year", type = 'viridis') +
labs(title = "Daily day-time average temperature in Berlin-Dahlem over time",
subtitle = "Model predictions in <span style='color:red'>red</span>.",
x = "Day of the year",
y = "Temperature in °C") +
theme(plot.subtitle = element_markdown())
We can confirm this conjecture quantitatively by calculating the mean error of our predictions \(\hat Y_t - Y_t\) for different decades:
(mean_err_per_decade <- mutate(meas_fit, d = round((year - 1900) / 10) * 10,
decade = as.ordered(ifelse(d < 100, paste0("19", d, "s"), sprintf("20%02ds", d - 100)))) |>
group_by(decade) |>
summarise(mean_error = mean(pred - temp)))
## # A tibble: 8 × 2
## decade mean_error
## <ord> <dbl>
## 1 1950s 0.288
## 2 1960s 0.827
## 3 1970s 0.494
## 4 1980s 0.508
## 5 1990s -0.0981
## 6 2000s -0.220
## 7 2010s -0.468
## 8 2020s -1.40
ggplot(mean_err_per_decade, aes(x = decade, y = mean_error)) +
geom_hline(yintercept = 0, linetype = "dashed") +
geom_point() +
scale_y_continuous(limits = c(-2, 2)) +
labs(title = "Mean prediction error per decade for m1",
x = "Decade",
y = "Prediction error in °C")
Figure 3: Mean prediction error per decade for m1
The reason for these systematic errors is the slight increase of the yearly average temperature as indicated by the trend line in figure 1. To put it bluntly: we didn’t account for global warming! We can do so by updating the model equation from model m1 (3) in order to include a term for a yearly linear change (i.e. increase) in temperature. Of course this is very simplified, but it should improve our previous model. So our updated model m2 is now:
\[ Y_t = \beta_0 + \beta_1 \cos(x_t) + \beta_2 \sin(x_t) + \beta_3 \text{year}_t + \epsilon_t. \]
And we can fit this updated model:
m2 <- lm(temp ~ cos(x) + sin(x) + year, meas)
summary(m2)
##
## Call:
## lm(formula = temp ~ cos(x) + sin(x) + year, data = meas)
##
## Residuals:
## Min 1Q Median 3Q Max
## -18.0982 -2.5367 -0.0541 2.5753 13.0459
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) -47.296595 2.091820 -22.61 <2e-16 ***
## cos(x) -9.010653 0.032010 -281.50 <2e-16 ***
## sin(x) -2.564623 0.031911 -80.37 <2e-16 ***
## year 0.028544 0.001053 27.11 <2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 3.724 on 27154 degrees of freedom
## Multiple R-squared: 0.7609, Adjusted R-squared: 0.7608
## F-statistic: 2.88e+04 on 3 and 27154 DF, p-value: < 2.2e-16
We can see that the fit is slightly better. \(R^2\) increased by about \(1\) percentage points, indicating that about \(1\%\) of the variation of the average daily temperature can be attributed to the yearly temperature increase. This doesn’t sound much, however, you should keep in mind that we’re talking about daily average temperatures which are influenced by a lot of factors.
The estimated coefficient for the yearly change is about \(0.0289\), which means that the we expect the yearly average temperature to increase by about \(0.289\text{°C}\) within \(10\) years, or about \(2.89\text{°C}\) within \(100\) years, which is indeed quite much.
Note also that our intercept has changed from about \(9.4\text{°C}\) to about \(-47.3\text{°C}\), because the model needs to account for the yearly temperature increase and hence predicts an average temperature of \(-47.3\text{°C}\) in year \(0\), while for example the average temperature in year \(2000\) is predicted as \(-47.3\text{°C} + 2000 \cdot 0.0289\text{°C} = 10.5\text{°C}\) (and \(39.4\text{°C}\) in year \(3000\)!). This of course shows that such simple models should never be used for extrapolation.
The model fit inspection plots didn’t change much:
plot(m2, which = 1:2, ask = FALSE)
We again check the model fit visually for a smaller time span:
meas_fit2 <- cbind(meas, pred = fitted(m2))
filter(meas_fit2, year >= 2018) |>
ggplot() +
geom_line(aes(date, temp), alpha = 0.25) +
geom_line(aes(date, pred), color = 'red') +
labs(title = "Daily day-time average temperature in Berlin-Dahlem since 2018",
subtitle = "Model predictions in <span style='color:red'>red</span>.",
x = "",
y = "Temperature in °C") +
theme(plot.subtitle = element_markdown())
And we also check it for the full time range. Here, we also see the linear increase in average temperature introduced in the updated model:
ggplot(meas_fit2) +
geom_line(aes(date, temp), alpha = 0.25) +
geom_line(aes(date, pred), color = 'red') +
labs(title = "Daily day-time average temperature in Berlin-Dahlem over time",
subtitle = "Model predictions in <span style='color:red'>red</span>.",
x = "",
y = "Temperature in °C") +
theme(plot.subtitle = element_markdown())
ggplot(meas_fit2, aes(day, temp, color = year)) +
geom_line(alpha = 0.25) +
geom_line(aes(day, pred, color = year, group = year)) +
scale_color_binned(type = 'viridis') +
labs(title = "Daily day-time average temperature in Berlin-Dahlem over time",
subtitle = "Model predictions as opaque colored curves.",
x = "Day of the year",
y = "Temperature in °C") +
theme(plot.subtitle = element_markdown())
As compared to model m1 (see figure 3), we don’t see the systematic underestimation of the temperature in the later decades anymore:
(mean_err_per_decade2 <- mutate(meas_fit2, d = round((year - 1900) / 10) * 10,
decade = as.ordered(ifelse(d < 100, paste0("19", d, "s"),
sprintf("20%02ds", d - 100)))) |>
group_by(decade) |>
summarise(mean_error = mean(pred - temp)))
## # A tibble: 8 × 2
## decade mean_error
## <ord> <dbl>
## 1 1950s -0.702
## 2 1960s 0.0655
## 3 1970s 0.0181
## 4 1980s 0.317
## 5 1990s -0.00329
## 6 2000s 0.161
## 7 2010s 0.198
## 8 2020s -0.468
ggplot(mean_err_per_decade2, aes(x = decade, y = mean_error)) +
geom_hline(yintercept = 0, linetype = "dashed") +
geom_point() +
scale_y_continuous(limits = c(-2, 2)) +
labs(title = "Mean prediction error per decade for m2",
x = "Decade",
y = "Prediction error in °C")
Figure 4: Mean prediction error per decade for m2
resid <- meas_fit2$temp - meas_fit2$pred
ggplot(data.frame(resid = resid), aes(resid)) +
geom_histogram(bins = 20)
quantile(abs(resid), 0.9)
## 90%
## 6.015373
thresh_unusal_temp <- 6
resid_stats <- group_by(meas_fit2, year) |>
summarise(me = mean(temp - pred),
mae = mean(abs(temp - pred)),
prop_days_warmer = mean(temp > pred + thresh_unusal_temp),
prop_days_colder = mean(temp < pred - thresh_unusal_temp))
#rmse = sqrt(mean((temp - pred)^2)))
resid_stats
## # A tibble: 75 × 5
## year me mae prop_days_warmer prop_days_colder
## <int> <dbl> <dbl> <dbl> <dbl>
## 1 1950 0.942 2.81 0.0932 0.0329
## 2 1951 1.26 2.83 0.0493 0
## 3 1952 0.00242 2.81 0.0492 0.0246
## 4 1953 1.56 3.04 0.112 0.0137
## 5 1954 -0.258 3.05 0.0493 0.0658
## 6 1955 -0.321 2.96 0.0384 0.0603
## 7 1956 -0.977 3.48 0.0328 0.104
## 8 1957 0.677 3.03 0.0904 0.0301
## 9 1958 0.169 2.48 0.0219 0.0164
## 10 1959 1.04 2.85 0.0822 0.0164
## # ℹ 65 more rows
resid_stats_plt <- pivot_longer(resid_stats, !year, names_to = "measure")
filter(resid_stats_plt, measure %in% c("mae", "me")) |>
ggplot(aes(x = year, y = value, fill = measure)) +
geom_col(position = position_dodge()) +
facet_wrap(vars(measure), nrow = 2, scales = "free_y")
filter(resid_stats_plt, measure %in% c("prop_days_warmer", "prop_days_colder")) |>
ggplot(aes(x = year, y = value, fill = measure)) +
geom_col(position = position_stack()) +
scale_fill_discrete(limits = rev)
resid_stats_ordered <- filter(resid_stats, year < 2024) |>
arrange(mae)
resid_stats_ordered |> head(1)
## # A tibble: 1 × 5
## year me mae prop_days_warmer prop_days_colder
## <int> <dbl> <dbl> <dbl> <dbl>
## 1 2017 -0.188 2.35 0.0274 0.0137
resid_stats_ordered |> tail(1)
## # A tibble: 1 × 5
## year me mae prop_days_warmer prop_days_colder
## <int> <dbl> <dbl> <dbl> <dbl>
## 1 1985 -1.20 3.55 0.0493 0.145
least_deviation_yr <- resid_stats_ordered |> head(1) |> pull(year)
most_deviation_yr <- resid_stats_ordered |> tail(1) |> pull(year)
least_most_plt <- data.frame(year = c(least_deviation_yr, most_deviation_yr), label = c("least deviation", "most deviation")) |>
inner_join(meas_fit2, by = 'year') |>
mutate(label = paste0(year, " (", label, ")"),
resid = temp - pred,
transparency = ifelse(abs(resid) > thresh_unusal_temp, 0.5, 0.1))
ggplot(least_most_plt, aes(day, temp, color = label)) +
geom_point(aes(alpha = transparency)) +
geom_line(aes(day, pred)) +
scale_color_discrete(guide = guide_legend(title = NULL)) +
scale_alpha_identity(guide = NULL)
ggplot(least_most_plt, aes(day, resid, color = label, alpha = transparency)) +
geom_hline(yintercept = 0, linetype = "dashed") +
geom_hline(yintercept = -thresh_unusal_temp, linetype = "dotted") +
geom_hline(yintercept = thresh_unusal_temp, linetype = "dotted") +
geom_point() +
scale_color_discrete(guide = guide_legend(title = NULL)) +
scale_alpha_identity(guide = NULL)
ggplot(least_most_plt, aes(day, temp, color = label)) +
geom_smooth(method = "loess", span = 0.2) +
geom_line(aes(day, pred), linetype = "dashed") +
scale_color_discrete(guide = guide_legend(title = NULL)) +
scale_alpha_identity(guide = NULL)
## `geom_smooth()` using formula = 'y ~ x'